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        Package&nbsp;moltk
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<h1 class="epydoc">Source Code for <a href="moltk-module.html">Package moltk</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"><tt class="py-comment">#    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt>  <tt class="py-line"><tt class="py-comment">#    Copyright (C) 2011  Christopher M. Bruns</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"><tt class="py-comment">#    This program is free software; you can redistribute it and/or modify</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-comment">#    it under the terms of the GNU General Public License as published by</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line"><tt class="py-comment">#    the Free Software Foundation; either version 2 of the License, or</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-comment">#    (at your option) any later version.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-comment">#    This program is distributed in the hope that it will be useful,</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"><tt class="py-comment">#    but WITHOUT ANY WARRANTY; without even the implied warranty of</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-comment">#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"><tt class="py-comment">#    GNU General Public License for more details.</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line"><tt class="py-comment">#    You should have received a copy of the GNU General Public License along</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line"><tt class="py-comment">#    with this program; if not, write to the Free Software Foundation, Inc.,</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"><tt class="py-comment">#    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line"><tt class="py-comment">#    </tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line"><tt class="py-comment">#    Commercial users should ask about our dual licensing model.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line"><tt class="py-comment">#    For questions contact: cmbruns@rotatingpenguin.com</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line"><tt class="py-comment"># moltk module docstring</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line"><tt class="py-docstring">moltk is the top level package of the MolTK tool kit, which provides tools for protein sequence/structure alignment and visualization.</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line"><tt class="py-docstring">The submodule "moltk.gui" contains the pure python moltk application and user interface.  </tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt>  <tt class="py-line"><tt class="py-docstring">The PySide package (http://www.pyside.org/) must be installed to use the moltk.gui package.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt>  <tt class="py-line"><tt class="py-docstring">Do not directly use the submodule "moltk._moltk", which represents the binary extension </tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt>  <tt class="py-line"><tt class="py-docstring">implemented in C++.  The top</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt>  <tt class="py-line"><tt class="py-docstring">level module "moltk" contains all of the symbols from "moltk._moltk", so use "import moltk"</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt>  <tt class="py-line"><tt class="py-docstring">of "from moltk import &lt;whatever&gt;" to get symbols from "moltk._moltk".</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt>  <tt class="py-line"><tt class="py-docstring">All MolTK code is Copyright (C) 2011  Christopher M. Bruns</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt>  <tt class="py-line"><tt class="py-docstring">This program is free software; you can redistribute it and/or modify</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt>  <tt class="py-line"><tt class="py-docstring">it under the terms of the GNU General Public License as published by</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt>  <tt class="py-line"><tt class="py-docstring">the Free Software Foundation; either version 2 of the License, or</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt>  <tt class="py-line"><tt class="py-docstring">(at your option) any later version.</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt>  <tt class="py-line"><tt class="py-docstring">This program is distributed in the hope that it will be useful,</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt>  <tt class="py-line"><tt class="py-docstring">but WITHOUT ANY WARRANTY; without even the implied warranty of</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt>  <tt class="py-line"><tt class="py-docstring">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt>  <tt class="py-line"><tt class="py-docstring">GNU General Public License for more details.</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt>  <tt class="py-line"><tt class="py-docstring">You should have received a copy of the GNU General Public License along</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt>  <tt class="py-line"><tt class="py-docstring">with this program; if not, write to the Free Software Foundation, Inc.,</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt>  <tt class="py-line"><tt class="py-docstring">51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt>  <tt class="py-line"><tt class="py-docstring">Commercial users should ask about our dual licensing model.</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt>  <tt class="py-line"><tt class="py-docstring">For questions contact: cmbruns@rotatingpenguin.com</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt>  <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Variable moltk._moltk=moltk-module.html#_moltk"><a title="moltk._moltk" class="py-name" href="#" onclick="return doclink('link-0', '_moltk', 'link-0');">_moltk</a></tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="moltk._moltk" class="py-name" href="#" onclick="return doclink('link-1', '_moltk', 'link-0');">_moltk</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt>  <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt>  <tt class="py-line"><tt class="py-comment"># Put documentation for _moltk members into moltk docs.</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt>  <tt class="py-line"><tt class="py-name">__all__</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt>  <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-2" class="py-name" targets="Variable moltk.s=moltk-module.html#s"><a title="moltk.s" class="py-name" href="#" onclick="return doclink('link-2', 's', 'link-2');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dir</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-3" class="py-name"><a title="moltk.s" class="py-name" href="#" onclick="return doclink('link-3', 's', 'link-2');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'_'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt>  <tt class="py-line">        <tt class="py-name">__all__</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method moltk.QueryPositionList.append()=moltk.QueryPositionList-class.html#append,Method moltk.TargetPositionList.append()=moltk.TargetPositionList-class.html#append,Method moltk.std_vector_int.append()=moltk.std_vector_int-class.html#append"><a title="moltk.QueryPositionList.append
moltk.TargetPositionList.append
moltk.std_vector_int.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="moltk.s" class="py-name" href="#" onclick="return doclink('link-5', 's', 'link-2');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt>  <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt>  <tt class="py-line"><tt class="py-comment"># moltk._moltk docstring</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt>  <tt class="py-line"><tt id="link-6" class="py-name"><a title="moltk._moltk" class="py-name" href="#" onclick="return doclink('link-6', '_moltk', 'link-0');">_moltk</a></tt><tt class="py-op">.</tt><tt class="py-name">__doc__</tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt>  <tt class="py-line"><tt class="py-string">Do not directly use the submodule "moltk._moltk".  Use module "moltk" instead.</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt>  <tt class="py-line"><tt class="py-string">The _moltk module provides tools for protein sequence/structure alignment and visualization.</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt>  <tt class="py-line"><tt class="py-string">This submodule "moltk._moltk" represents the binary extension implemented in C++.  The top</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt>  <tt class="py-line"><tt class="py-string">level module "moltk" contains all of the symbols from "moltk._moltk", so use "import moltk"</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt>  <tt class="py-line"><tt class="py-string">of "from moltk import &lt;whatever&gt;" to get symbols from "moltk._moltk".</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt>  <tt class="py-line"><tt class="py-string">All MolTK code is Copyright (C) 2011  Christopher M. Bruns</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt>  <tt class="py-line"><tt class="py-string">This program is free software; you can redistribute it and/or modify</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt>  <tt class="py-line"><tt class="py-string">it under the terms of the GNU General Public License as published by</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt>  <tt class="py-line"><tt class="py-string">the Free Software Foundation; either version 2 of the License, or</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt>  <tt class="py-line"><tt class="py-string">(at your option) any later version.</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt>  <tt class="py-line"><tt class="py-string">This program is distributed in the hope that it will be useful,</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt>  <tt class="py-line"><tt class="py-string">but WITHOUT ANY WARRANTY; without even the implied warranty of</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt>  <tt class="py-line"><tt class="py-string">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt>  <tt class="py-line"><tt class="py-string">GNU General Public License for more details.</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt>  <tt class="py-line"><tt class="py-string">You should have received a copy of the GNU General Public License along</tt> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt>  <tt class="py-line"><tt class="py-string">with this program; if not, write to the Free Software Foundation, Inc.,</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt>  <tt class="py-line"><tt class="py-string">51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</tt>  <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt>  <tt class="py-line"><tt class="py-string">Commercial users should ask about our dual licensing model.</tt> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt>  <tt class="py-line"><tt class="py-string">For questions contact: cmbruns@rotatingpenguin.com</tt> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt>  <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L90"></a><tt class="py-lineno">90</tt>  <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno">91</tt>  <tt class="py-line"><tt class="py-comment"># Hide _moltk submodule</tt> </tt>
<a name="L92"></a><tt class="py-lineno">92</tt>  <tt class="py-line"><tt id="link-7" class="py-name"><a title="moltk._moltk" class="py-name" href="#" onclick="return doclink('link-7', '_moltk', 'link-0');">_moltk</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L93"></a><tt class="py-lineno">93</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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